An in vitro, in utero and in silico framework of oxygen diffusion in intricate vascular networks of the placenta

The placenta is a temporary and complex organ critical for fetal development through its subtle but convoluted harmonization of endocrine, vascular, haemodynamic and exchange adaptations. Yet, due to experimental, technological and ethical constraints, this unique organ remains poorly understood. In silico tools are emerging as a powerful means to overcome these challenges and have the potential to actualize novel breakthroughs. Here, we present an interdisciplinary framework combining in vitro experiments used to develop an elegant and scalable in silico model of oxygen diffusion. We then use in utero imaging of placental perfusion and oxygenation in both control and growth-restricted rodent placentas for validation of our in silico model. Our framework revealed the structure-function relationship in the feto-placental vasculature; oxygen diffusion is impaired in growth-restricted placentas, due to the diminished arborization of growth-restricted feto-placental vasculature and the lack of decelerated flow for adequate oxygen diffusion and exchange. We highlight the mechanisms of impairment in a rat model of growth restriction, underpinned by placental vascular impairment. Our framework reports and validates the prediction of blood flow deceleration impairment in growth restricted placentas with the placenta's oxygen transfer capability being significantly impaired, both globally and locally. Key words: Placenta; fetal growth restriction; oxygen diffusion; computational fluid dynamics; MRI

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Usefulness of collaboration between mathematical models and cell engineering for elucidating complex disease mechanisms and discover effective drugs

European Heart Journal ◽

10.1093/ehjci/ehaa946.3600 ◽

2020 ◽

Vol 41 (Supplement_2) ◽

Author(s):

H Kohjitani ◽

A Kashiwa ◽

T Makiyama ◽

F Toyoda ◽

Y Yamamoto ◽

...

Keyword(s):

Mathematical Model ◽

In Silico ◽

Complex Disease ◽

Ion Selectivity ◽

Public Institution ◽

Cell Engineering ◽

Funding Source ◽

Patch Clamp Technique ◽

In Silico Model

Abstract Background A missense mutation, CACNA1C-E1115K, located in the cardiac L-type calcium channel (LTCC), was recently reported to be associated with diverse arrhythmias. Several studies reported in-vivo and in-vitro modeling of this mutation, but actual mechanism and target drug of this disease has not been clarified due to its complex ion-mechanisms. Objective To reveal the mechanism of this diverse arrhythmogenic phenotype using combination of in-vitro and in-silico model. Methods and results Cell-Engineering Phase: We generated human induced pluripotent stem cell (hiPSC) from a patient carrying heterozygous CACNA1C-E1115K and differentiated into cardiomyocytes. Spontaneous APs were recorded from spontaneously beating single cardiomyocytes by using the perforated patch-clamp technique. Mathematical-Modeling Phase: We newly developed ICaL-mutation mathematical model, fitted into experimental data, including its impaired ion selectivity. Furthermore, we installed this mathematical model into hiPSC-CM simulation model. Collaboration Phase: Mutant in-silico model showed APD prolongation and frequent early afterdepolarization (EAD), which are same as in-vitro model. In-silico model revealed this EAD was mostly related to robust late-mode of sodium current occurred by Na+ overload and suggested that mexiletine is capable of reducing arrhythmia. Afterward, we applicated mexiletine onto hiPSC-CMs mutant model and found mexiletine suppress EADs. Conclusions Precise in-silico disease model can elucidate complicated ion currents and contribute predicting result of drug-testing. Funding Acknowledgement Type of funding source: Public Institution(s). Main funding source(s): Japan Society for the Promotion of Science, Grant-in-Aid for Young Scientists

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Prediction of Oral Bioavailability in Rats: Transferring Insights from in Vitro Correlations to (Deep) Machine Learning Models Using in Silico Model Outputs and Chemical Structure Parameters

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.9b00460 ◽

2019 ◽

Vol 59 (11) ◽

pp. 4893-4905 ◽

Cited By ~ 7

Author(s):

Sebastian Schneckener ◽

Sergio Grimbs ◽

Jessica Hey ◽

Stephan Menz ◽

Maren Osmers ◽

...

Keyword(s):

Machine Learning ◽

Oral Bioavailability ◽

In Silico ◽

Chemical Structure ◽

Structure Parameters ◽

Learning Models ◽

In Silico Model ◽

Machine Learning Models

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The Pseudomonas Quorum-Sensing Regulator RsaL Belongs to the Tetrahelical Superclass of H-T-H Proteins

Journal of Bacteriology ◽

10.1128/jb.01552-06 ◽

2006 ◽

Vol 189 (5) ◽

pp. 1922-1930 ◽

Cited By ~ 32

Author(s):

Giordano Rampioni ◽

Fabio Polticelli ◽

Iris Bertani ◽

Karima Righetti ◽

Vittorio Venturi ◽

...

Keyword(s):

Dna Binding ◽

Quorum Sensing ◽

In Silico ◽

Mobility Shift ◽

Specific Domain ◽

Signal Molecule ◽

In Silico Model ◽

Opportunistic Human Pathogen

ABSTRACT In the opportunistic human pathogen Pseudomonas aeruginosa, quorum sensing (QS) is crucial for virulence. The RsaL protein directly represses the transcription of lasI, the synthase gene of the main QS signal molecule. On the basis of sequence homology, RsaL cannot be predicted to belong to any class of characterized DNA-binding proteins. In this study, an in silico model of the RsaL structure was inferred showing that RsaL belongs to the tetrahelical superclass of helix-turn-helix proteins. The overall structure of RsaL is very similar to the N-terminal domain of the lambda cI repressor and to the POU-specific domain of the mammalian transcription factor Oct-1 (Oct-1 POUs). Moreover, residues of Oct-1 POUs important for structural stability and/or DNA binding are conserved in the same positions in RsaL and in its homologs found in GenBank. These residues were independently replaced with Ala, and the activities of the mutated variants of RsaL were compared to that of the wild-type counterpart in vivo by complementation assays and in vitro by electrophoretic mobility shift assays. The results validated the RsaL in silico model and showed that residues Arg 20, Gln 38, Ser 42, Arg 43, and Glu 45 are important for RsaL function. Our data indicate that RsaL could be the founding member of a new protein family within the tetrahelical superclass of helix-turn-helix proteins. Finally, the minimum DNA sequence required for RsaL binding on the lasI promoter was determined, and our data support the hypothesis that RsaL binds DNA as a dimer.

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Rational Design of a Triple-Layered Coaxial Extruder System: in silico and in vitro Evaluations Directed Towards Optimizing Cell Viability

International Journal of Bioprinting ◽

10.18063/ijb.v6i4.282 ◽

2020 ◽

Vol 6 (4) ◽

Author(s):

Christian Augusto Silva ◽

Carlos J Cortés-Rodriguez ◽

Jonas Hazur ◽

Supachai Reakasame ◽

Aldo R. Boccaccini

Keyword(s):

Cell Viability ◽

In Silico ◽

Rational Design ◽

Three Dimensional ◽

Complex Structures ◽

Vascular Networks ◽

Coaxial Nozzle ◽

Wide Availability ◽

Cell Functionality

Biofabrication is a rapidly evolving field whose main goal is the manufacturing of three-dimensional (3D) cell-laden constructs that closely mimic tissues and organs. Despite recent advances on materials and techniques directed toward the achievement of this goal, several aspects such as tissue vascularization and prolonged cell functionality are limiting bench-to-bedside translation. Extrusion-based 3D bioprinting has been devised as a promising biofabrication technology to overcome these limitations, due to its versatility and wide availability. Here, we report the development of a triple-layered coaxial nozzle for use in the biomanufacturing of vascular networks and vessels. The design of the coaxial nozzle was first optimized toward guaranteeing high cell viability upon extrusion. This was done with the aid of in silico evaluations and their subsequent experimental validation by investigating the bioprinting of an alginate-based bioink. Results confirmed that the values for pressure distribution predicted by in silico experiments resulted in cell viabilities above 70% and further demonstrated the effect of layer thickness and extrusion pressure on cell viability. Our work paves the way for the rational design of multi-layered coaxial extrusion systems to be used in biofabrication approaches to replicate the very complex structures found in native organs and tissues.

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Exploration of the Mixing Phenomena during Interaction of Internal and External Circulations (EMPACs): Developing an in-vitro and in-silico Model of the Human Circulation

The Thoracic and Cardiovascular Surgeon ◽

10.1055/s-0036-1571485 ◽

2016 ◽

Vol 64 (S 01) ◽

Author(s):

P. Grieshaber ◽

J. Gehron ◽

M. Bongert ◽

S. Schäfer ◽

M. Fiebich ◽

...

Keyword(s):

In Silico ◽

In Silico Model

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In-silico model of skin penetration based on experimentally determined input parameters. Part II: Mathematical modelling of in-vitro diffusion experiments. Identification of critical input parameters

European Journal of Pharmaceutics and Biopharmaceutics ◽

10.1016/j.ejpb.2007.05.018 ◽

2008 ◽

Vol 68 (2) ◽

pp. 368-379 ◽

Cited By ~ 47

Author(s):

Arne Naegel ◽

Steffi Hansen ◽

Dirk Neumann ◽

Claus-Michael Lehr ◽

Ulrich F. Schaefer ◽

...

Keyword(s):

Mathematical Modelling ◽

In Silico ◽

Skin Penetration ◽

In Silico Model ◽

In Vitro Diffusion ◽

Input Parameters

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A local mechanism generates saturation in an in silico model of in vitro multicellular tumor spheroid growth

Journal of Critical Care ◽

10.1016/j.jcrc.2007.10.002 ◽

2007 ◽

Vol 22 (4) ◽

pp. 331

Author(s):

Jesse A. Engelberg ◽

C. Anthony Hunt

Keyword(s):

In Silico ◽

Tumor Spheroid ◽

Multicellular Tumor Spheroid ◽

In Silico Model ◽

Local Mechanism ◽

Spheroid Growth

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The effect of nicotine on in vitro placental perfusion pressure

Canadian Journal of Physiology and Pharmacology ◽

10.1139/y06-037 ◽

2006 ◽

Vol 84 (8-9) ◽

pp. 953-957 ◽

Cited By ~ 11

Author(s):

Shannon A. Bainbridge ◽

Graeme N. Smith

Keyword(s):

Vascular Function ◽

Perfusion Pressure ◽

Growth Restriction ◽

Placental Perfusion ◽

Normal Term ◽

Increased Risk ◽

Uterine Growth ◽

Elective Cesarean ◽

Placental Blood

Cigarette smoking throughout pregnancy is associated with several negative outcomes, of which an increased incidence of intra-uterine growth restriction (IUGR) is most pronounced. Gestationally age-matched infants born to smoking mothers are, on average, 200 g lighter at birth, per pack smoked per day. The mechanisms and specific tobacco compounds responsible for the increased risk of IUGR among smokers have yet to be identified; however, it is widely accepted that smoking women have compromised placental perfusion throughout gestation due to the vasoconstricting effect of nicotine on uterine and placental blood vessels. Despite the universal acceptance of this theory, very little work has been completed to date examining the vasoactive properties of nicotine within the human placenta. The objective of this study was to determine the effect of nicotine on placental vascular function. Normal-term human placentae were obtained after elective cesarean sections. An in vitro placental perfusion system was used; increasing doses of nicotine (20–240 ng/mL) were added to either the maternal (n = 5) or fetal (n = 3) circulation. The basal feto-placental perfusion pressure was 39.87 ± 4.3 mmHg and was not affected by nicotine. This finding supports the hypotheses that nicotine does not directly affect placental microvascular function and that any contribution to fetal growth restriction is likely at the level of placental function (i.e., amino acid transport) and (or) uterine vascular function.

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